Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer

Basak, Sujit; Sakia, Nabanita; Dougherty, Laura; Guo, Zhuojun; Wu, Fang; Mindlin, Frank A.; Lary, Jeffrey W.; Cole, James L.; Ding, Feng; Bowen, Mark E.

doi:10.1016/j.jmb.2020.166793

Cited by 19 publications

(24 citation statements)

References 95 publications

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“… 87 Generalized ensemble methods such as rxDMD 88 coupled with the implicit solvent accelerates the sampling of the conformational dynamics of biomolecules 89 and have been shown to have high predictive power in capturing the structure and dynamics of folded protein, protein-protein interactions, and supertertiary structure of proteins in vitro and in live cells. 90 – 92 …”

Section: Resultsmentioning

confidence: 99%

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

Saikia

Yanez-Orozco

Qiu

et al. 2021

Cell Reports Physical Science

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SUMMARY SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.

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Section: Resultsmentioning

confidence: 99%

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

Saikia

Yanez-Orozco

Qiu

et al. 2021

Cell Reports Physical Science

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“…Discrete molecular dynamics (DMD) is a special category of molecular dynamics (MD) where the conventional MD force field is remodeled as discrete step functions. [ 21 ] DMD simulations have been widely applied to biomolecular studies such as protein aggregation, [ 22 ] protein structure and dynamics, [ 23 ] and protein‐nanoparticle interactions. [ 24 ] Here, the bonded (i.e., bonds, bond angle, and dihedral angle) and non‐bonded terms (van der Waals, electrostatic, solvation, and hydrogen bonds) comprised the inter‐atomic potential for DMD simulations.…”

Section: Methodsmentioning

confidence: 99%

A Framework of Paracellular Transport via Nanoparticles‐Induced Endothelial Leakiness

Lee

Tang

et al. 2021

Advanced Science

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Nanomaterial‐induced endothelial leakiness (NanoEL) is an interfacial phenomenon denoting the paracellular transport of nanoparticles that is pertinent to nanotoxicology, nanomedicine and biomedical engineering. While the NanoEL phenomenon is complementary to the enhanced permeability and retention effect in terms of their common applicability to delineating the permeability and behavior of nanoparticles in tumoral environments, these two effects significantly differ in scope, origin, and manifestation. In the current study, the descriptors are fully examined of the NanoEL phenomenon elicited by generic citrate‐coated gold nanoparticles (AuNPs) of changing size and concentration, from microscopic gap formation and actin reorganization down to molecular signaling pathways and nanoscale interactions of AuNPs with VE‐cadherin and its intra/extracellular cofactors. Employing synergistic in silico methodologies, for the first time the molecular and statistical mechanics of cadherin pair disruption, especially in response to AuNPs of the smallest size and highest concentration are revealed. This study marks a major advancement toward establishing a comprehensive NanoEL framework for complementing the understanding of the transcytotic pathway and for guiding the design and application of future nanomedicines harnessing the myriad functions of the mammalian vasculature.

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“…DMD simulations for amyloid and EC1 cadherin dimer binding: All-atom discrete molecular dynamics (DMD) simulation with implicit solvent models was used for this study to characterize the Aβ induced VEcadherin dissociation. DMD is a unique category of molecular dynamics (MD) with signi cantly enhanced sampling e ciency, which has been widely applied to biomolecular studies such as protein folding, peptide aggregation [67][68][69] , and understanding the protein structure and dynamics 70,71 . The details of the DMD algorithm were described in our previous studies [67][68][69] .…”

Section: Ex Vivo Vascular Leakiness Assaymentioning

confidence: 99%

Endothelial Leakiness Induced by Amyloid Protein Aggregation

Lee

et al. 2022

Preprint

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Alzheimer’s disease (AD) is a major cause of dementia debilitating the global ageing population. Current understanding of the AD pathophysiology implicates the aggregation of amyloid beta (Aβ) as causative to neurodegeneration, with tauopathies and neuroinflammation considered as other major culprits. Curiously, vascular endothelial barrier dysfunction is strongly associated with Aβ deposition and 80-90% AD subjects also experience cerebral amyloid angiopathy. Here we show amyloid proteins-induced endothelial leakiness (APEL) in human microvascular endothelial monolayers as well as in mouse cerebral vasculature. Using signaling pathway assays and discrete molecular dynamics, we revealed that the angiopathy first arose from a disruption to vascular endothelial (VE)-cadherin junctions exposed to the nanoparticulates of Aβ oligomers and seeds, preceding the earlier implicated proinflammatory and pro-oxidative stressors to endothelial leakiness. These findings are analogous to nanomaterials-induced endothelial leakiness (NanoEL), a major phenomenon in nanomedicine depicting the paracellular transport of anionic inorganic nanoparticles in the vasculature. As APEL also occurred with the anionic seeds of pathogenic alpha synuclein and functional FapC bacterial amyloid, this study projects a general new paradigm for elucidating the vascular permeation, systemic spread, and cross-seeding of amyloid proteins that underlie the pathogeneses of AD, Parkinson’s, as well as a range of amyloid diseases.

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Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer

Cited by 19 publications

References 95 publications

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

A Framework of Paracellular Transport via Nanoparticles‐Induced Endothelial Leakiness

Endothelial Leakiness Induced by Amyloid Protein Aggregation

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